knitr::opts_knit$set(root.dir = rprojroot::find_rstudio_root_file())
knitr::opts_chunk$set(echo = F, warning = F, message = F)

seu_merge_epi_p009t1_strict_epi_p009t2_strict_epi_p013t_strict_epi_p014t_strict_epi_p009ot0_strict_epi_p009ot2_strict_epi_p013ot0_strict_epi_p013ot3_strict_epi_p014ot0_strict.rds

Signature scoring

## [1] "p009t1"  "p009t2"  "p013t"   "p014t"   "p009ot0" "p009ot2" "p013ot0"
## [8] "p013ot3" "p014ot0"
## [1] "broad done"
## [1] "morkel done"
## [1] "SMAD done"
## [1] "TNFa done"
## [1] "Wnt done"
## [1] "YAP done"
## [1] "regev done"

Louvain clusters

Cluster marker genes

rank 0 1 10 11 12 13 14 15 16 2 3 4 5 6 7 8 9
1 TM4SF4 RPS7 PMEPA1 NXPE1 PRSS56 PLA2G2A MAP2 AQP5 AC136475.3 HIST1H4C CLCA4 FABP1 TM4SF4 TESC SPINK4 CCL20 MT-ND2
2 RPS27 RPS4X CEACAM6 B3GNT7 ATAD5 OLFM4 MMP7 XIST AL137077.2 TUBB SELENOP CKB FABP1 LDHB MUC2 AREG MT-ND4
3 RPS21 C9orf16 CD24 PLA2G2A IGF2BP1 PIGR COL6A1 PGGHG ARC TUBA1B GUCA2A NDUFA4L2 ANXA10 TUBA1B ZG16 CXCL1 MT-ATP6
4 MT-ATP8 RPS18 ZBTB20 PIGR MCM4 LEFTY1 UPK2 MUC6 HIST1H2BG H2AFZ SLC26A3 LDHA CTSE RPL7A FCGBP TM4SF4 MT-CO3
5 ROMO1 RPS13 FN1 LEFTY1 PMEPA1 B3GNT7 MAP1B AC136475.3 Z93241.1 UBE2C CEACAM7 PGK1 REG4 RPL35 ITLN1 TM4SF1 IGKC
6 RPL7A IFITM3 MUC4 CENPJ HSPA1A C6orf15 SLC28A3 HEXIM1 RANBP1 CA1 CSTB ABCG2 RPSA TFF3 KLK10 ALPK3
7 RPS23 DPEP1 MT-ND1 FN1 NUPR1 GPC1 AC020656.1 SOCS1 HMGB1 PLAC8 MIR210HG ADIRF H2AFZ CLCA1 CXCL3 MT-CO2
8 RPL10A MACC1 MT-CO3 BRCA2 AGR3 LEMD1 BST2 JUN PCNA TSPAN1 SCD LGALS3 RPL39L SERPINA1 KLK7 MT-ND1
9 RPL10 CEL OLFM4 IFITM3 PRAC1 KRT23 CA9 IER5L HIST1H1B CA2 GAPDH TFF1 RAN ST6GALNAC1 ANXA2 MT-ND3
10 RPS12 SDC4 MT-CO1 XRCC2 NXPE1 TACSTD2 ONECUT3 RASD1 UBE2T PHGR1 C4orf3 MMP1 NCL REP15 CXCL2 MT-ND5
11 RPL30 ATP9A MT-ATP6 ERAP2 NXPE4 PERP LYZ PPP1R15A HMGB2 GUCA2B DBI PHGR1 ATP5MC3 REG4 REG4 MT-CO1
12 RPS14 PERP MT-ND3 DHFR MT1M UCA1 TPM2 HIST1H4A TOP2A PIGR FAM162A PSCA SET WFDC2 PHLDA2 COL27A1
13 RPS2 IGKC MT-CO2 ALPK3 MUC4 S100A4 HLA-DPA1 FOSB MCM3 MUC12 TPI1 S100A6 HSPD1 KLK1 S100A14 MT-ND4L
14 RPS15A SLC2A12 MT-ND4 HELLS SULT1B1 TMEM47 OLFM4 AL031777.3 GINS2 AQP8 RPL11 S100P NAP1L1 GSN GDF15 PRSS56
15 RPLP1 RPL13 PRAC1 BRCA1 ADH1C PI3 CD74 BTG2 TPX2 IFI27 NDRG1 ONECUT3 EIF4EBP1 SPINK1 S100P PMEPA1
16 RPL11 RAB11FIP1 MT-ND2 NPTX2 HMGCS2 ANXA1 HLA-DRA EGR1 MKI67 CDHR5 LCN15 AC020656.1 CLDN2 HSPA1A MALAT1 FN1
17 RPL24 PLS3 NXPE4 TOP2A RPS4Y1 S100A11 BMP4 EGR3 DTYMK CD177 RPL7A HPGD IGFBP2 MUC4 TNFRSF12A RNF213
18 RPL7 KRT17 MT-ND5 LMNB1 SI SLC2A1 CAPN12 AL360012.1 DNMT1 MT-CO1 IGFBP2 HSD17B2 LSM3 KLF4 HES1 GAS6-AS1
19 RPL23 JUP IGKC CENPF SLC28A2 TNFRSF12A PKDCC SOX4 MCM7 ITM2C PKM KLK7 NDUFA8 NUPR1 TSPAN8 HSPA1B
20 RPL32 ACTG1 NUPR1 HMGB1 UGT2A3 KRT80 MUC5AC CSKMT MYBL2 FXYD3 RPS4X TSPAN8 PTMS RASD1 ARGLU1
21 RPS3 ACE2 MUC12 GAL VSIG2 IL18 EPHB3 AL355075.4 GMNN SGK1 REN KRT20 LCN2 SYTL2 CENPJ
22 RPL5 HSPA1B DMBT1 MKI67 SEMA6A PDLIM4 REG1A HIST1H2AH TYMS CEACAM1 RPS14 LGALS4 RPL24 IGKC SOX4
23 RPL13 RPL34 SI ZIC2 MT1E PHLDA3 DPP4 IER5 BRCA2 MS4A12 RPS7 SLPI RPL6 FRYL ENGASE
24 RPL35A NPTX2 MT-ND4L CDC6 CA2 BASP1 ADGRG6 MAFB TK1 MT-ND3 NACA TFF2 HSP90AB1 SPDEF MT-ATP8
25 NACA WNT11 HSPA1A MCM7 SLC4A4 TIMP2 PIGR RGS16 MAD2L1 MT-ATP6 RPS18 FXYD3 RPL21 KIAA1324 MACC1
26 RPS27A PROX1 SLC4A4 CDT1 CREB3L1 C9orf16 MUC17 IER2 CLSPN MT-ND5 RPL32 AKR1C3 CD81 CREB3L1 KCNQ1OT1
27 RPL21 NORAD CA2 MCM3 SPINK1 ATP6V1G1 MUC5B HIST1H2AG CDK1 DUOX2 RPS27A UQCRQ RPS2 MLPH JUN
28 RPS6 HSPH1 PLCE1 KIF4A DMBT1 CLIC3 SYNE2 PGGHG HIST2H2AC MT-ND1 RPL10 SH3BGRL3 MRPL51 HEPACAM2 VEGFA
29 RPS16 VEGFA B3GALT5 CIP2A C15orf48 ANXA3 CXCL8 HIST1H3A ZWINT PLA2G2A ATP5MC3 KLK11 RPL8 B3GNT6 RNF43
30 RPL12 CDH1 SULT1B1 PTPRO FAM3D DCBLD2 REG1B JUNB HELLS CA4 RPS19 ANPEP HMGB1 PIGR MTRNR2L12
31 RPS20 SRPX2 VSIG2 BIRC5 TMEM176B KLK6 COL17A1 HSPA1B FAM111B SDCBP2 RPS13 CEACAM6 RPL27 ENTPD8 ATAD5
32 RPL27 RPL28 PPP1R12B GINS2 BMP2 KRT17 REG3A C2CD4B CENPU MT-ND2 FDFT1 MALAT1 NACA ATP2A3 MKI67
33 SSR4 EIF4A2 MT1E ECT2 RARRES1 GGH KLK10 DNAJB1 FBXO5 MDK RPS23 PLA2G16 SNRPB ERN2 ENC1
34 LAMP1 CREB5 MT-ATP8 MCM2 GOLM1 TMSB4X TMC5 BTG1 HIST1H1D C2orf88 RPS16 TXN TUBB4B ATOH1 ANO9
35 RPL6 PTBP3 HMGCS2 CDCA7 LGALS2 UBE2E2 SLCO4A1-AS1 PPP1R10 PTMA PKIB RPS3 ALDH1A1 LCN15 RAB27A IER5L
36 NDUFA4 EPB41L1 PCK1 IGKC PRKACB BFSP1 MT-ATP8 VEGFA MCM6 GPA33 S100A14 MYL12B RPL32 TPSG1 TRIM44
37 PRDX1 SOX9 MT1M CEL MUC12 PCCA DMBT1 RHOB BIRC5 AOC1 RPL8 ANXA2 ATP5MC1 VSIG2 CENPF
38 RPL3 CANX SPINK1 ONECUT2 SPINK5 LCN2 MT-ND4L MALAT1 SNRNP25 SAMD9 RPL35A S100A14 RPLP0 GALNT5 SETX
39 RPL23A EPSTI1 MUC5B NOTCH1 MAOA LINC00520 AGR3 ID4 MCM4 SMIM22 RPS5 KLK10 YBX1 PRAC1 ATRX
40 ZFAS1 ENC1 TFCP2L1 SET TCEA3 MSLN SERPINA1 TCIM CDT1 MT-CO2 RPS2 PHLDA2 PRDX4 NXPE1 SPEN
41 RPL8 DSP FRYL ATAD2 RHBDL2 MSX2 IGFBP3 FOS RRM1 MISP RPL7 S100A16 RANBP1 BCAS1 HEXIM1
42 RPL13A TMEM176A MTRNR2L12 SMC4 GLUL BAMBI HSPG2 PLK2 ATAD2 TMPRSS2 RPSA SLC40A1 MRPS26 RAP1GAP LUC7L3
43 RPL39 TFF3 MT1G NCAPD2 PLA2G10 KRT18 SLC40A1 IER3 NASP SLC4A4 SLC25A5 SLC22A18 HSP90AA1 L1TD1 IER3
44 RACK1 MBNL2 ATP2A3 TK1 ATP2A3 ANXA2 CEMIP2 LINC02432 RAN CDKN2B-AS1 RPL5 MT-ATP8 HSPE1 DNAJC12 ZFP36L2
45 ASCL2 KRT80 FAM3D WDR34 TMEM176A CHPF KCNN4 CD74 RFC4 MT-ND4L RPL21 CCND2 RPS7 ANO7 DNAJB1
46 RPL4 YWHAZ NFKBIZ SPINK1 HOXB13 CNN3 PLA2G16 ARGLU1 DUT MT-CO3 RPL24 ETHE1 RPL5 PRUNE2 VMP1
47 RPSA IRF2BP2 AC254629.1 MSH6 KCTD12 UBC AGR2 GADD45B DEK SLC9A3 RPL18A POLR2L SNRPF FMOD
48 RPS5 LRP4 ZFP36L2 IPO5 AMN TUBA1A MT-ND5 CDKN1C E2F1 MT1M RPS6 CBR1 RPS4X NEURL1
49 RPL29 RPS15A AMN ORC6 FOS EIF1 KLK6 TRIM44 CCNA2 AMN CD81 RPL7 FAM177B
50 RPL18A ANXA4 AGR3 PCNA CTSS CST3 MSLN HIST1H2BH RFC2 MT-ND4 PYCARD NPM1 BEST2
51 RPL27A SOX4 ELF3 FANCI C10orf99 FOLR1 CCNL2 JUND LDHB PDE9A MIF CCT7 B4GALNT2
52 CD81 GAS6-AS1 PDCD4 CCDC34 CDC42EP5 JUP LAMB1 XIST MND1 MXI1 RPLP1 MRPL41 RETNLB
53 RPS19 CEACAM5 CLMN GOLIM4 PPP1R12B CD9 CCND2 HIST1H4E DIAPH3 VSIG2 PRDX5 PTTG1 ALDH1L1
54 RPS9 TMEM176B FOS RAD51AP1 TFCP2L1 TRIM29 SLC12A2 HES1 FABP5 ABCA5 CLIC1 ASCL2 AQP3
55 LCN2 FOXQ1 AKAP9 SMC1A HLA-DRA CCND1 BACE2 NRARP ASF1B SLC26A2 RPL12 RPS27A CAPN9
56 TALDO1 TOB1 CA12 HSPA1B PGM2L1 TMSB10 NKTR CEBPB SMC4 TMIGD1 RPL6 C1QBP RAB26
57 RPS8 ZFP36L1 JCHAIN HNRNPD ITM2C SAT1 EGLN3 TPM2 SNRPG CDKN2B ENO1 RPL11 SCGB2A1
58 POMP RPS3A ERN2 NAA50 CA12 KRT8 ABHD2 ZFP36L2 TEX30 PLA2G10 PCCA ODC1 DLL1
59 RPL37 RPL23A IVNS1ABP EPHB3 PALLD KRT19 GCC2 OLFM4 RPA3 CYP3A5 RPS12 HMGB3 SMAD9
60 FTH1 RPL10 UGT2B17 PAICS NFKBIZ ATP6V0E1 SPNS2 REG1A SLBP AC023157.3 RPL3 PTGES3 PLXDC2
61 GSTP1 TM4SF1 HLA-DRA KIF20B CCL28 RHOC EEF2 RPL28 TOMM40 DHRS9 ACOT13 RPLP2 FAM3D
62 EIF1 TMEM123 TCIM HNRNPA3 B3GALT5 FLNA PHLDA1 GOLGA8A HSPD1 SMPDL3A EIF1 CNBP FOXA3
63 RPS3A RPL31 GOLM1 PBK EDN3 GSTP1 APOL1 CITED2 CENPM MEP1A RACK1 PSMB1 SCNN1A
64 EEF1B2 FNDC3B NKTR RRM1 MUC5B SEMA3B H1F0 GADD45G ANP32B MXD1 LGALS4 TMSB10 TCEA3
65 UQCRB PTPRO FOSB ACE2 KLF5 MLF1 ATP1B1 PMAIP1 CENPK SCNN1B EEF1B2 SSBP1 ANXA13
66 CST3 HLA-C JUNB CHEK1 PDCD4 ATP6V1F TRAF5 GDF15 SNRPD1 USP53 TMSB4X RPS13 TCIM
67 RPLP2 RPL21 VMP1 RPL35 LRRC19 LAMP1 TBX3 ELF3 FANCI TRPM6 RPL27 RPL23A CDC42EP5
68 COL9A3 ZFAS1 GLUL FOXM1 METTL7A S100A14 DSG2 MYADM ACAT2 SLC17A4 EBP EIF5A MT-ND3
69 TPT1 HLA-E JUN DEK AGR2 KRT6B REG4 RNF213 NUCKS1 C1QTNF12 POMP CCT2 AKAP9
70 EEF1A1 PTK7 ZFP36 DPEP1 SELENOP GUK1 ITGA6 CXCL8 ORC6 ACVRL1 RPLP2 PRKDC MCF2L
71 SLC25A6 ARMCX3 CDC42EP5 PRKDC FOSB TMED9 FAT1 AC108134.2 HNRNPAB TMEM37 RPL39 GAPDH FABP2
72 ATP5MC3 TPT1 SRGN NOP56 PLCE1 GSN TFF1 ATF3 NPM1 DDX60 COX7B CKS2 XBP1
73 EIF3H RCN1 SYNE2 CLSPN ST6GALNAC1 COL9A3 DUOX2 AL118516.1 NCAPG HHLA2 CD9 PCCA FOS
74 MGST3 RPS21 MT1X HMGA1 PCK1 VSNL1 APP CLDN4 HSPE1 RETREG1 RPS9 FABP5 MT-ND2
75 FTL SLC12A2 BTG1 BAG2 SLC6A14 DSP CTSE CCDC88B CDC6 XDH INSIG1 RPS20 MT-ND1
76 YBX1 SORBS1 HEXIM1 FBL MT2A REN PDZK1IP1 RPL13 NCL CCDC68 COX7A2 TUBB MT1G
77 PARK7 IER3 TSC22D3 SLC12A2 ELF3 CADM1 F3 ZFP36 PDCD5 ENTPD8 QPRT POMP HSPA2
78 CLIC1 RPS12 RMI2 TC2N KLK10 LAMC2 AC023157.3 LSM2 CDHR2 VDAC1 SLC25A5 SIDT1
79 HINT1 IFI27 CDC20 MT1F SQSTM1 NDRG1 DUSP1 BTG3 RARRES3 ACSL3 PRMT1 FOSB
80 PERP FOXO3 BAZ1B RNF186 CSTB ANXA1 NKTR CENPW SULT1B1 RPL10A GTF3A FAM107B
81 PEBP1 PLOD2 SMC2 KLF9 RPL7A CD55 RPS19 SMC2 SLC51B EPCAM SSB CRACR2A
82 GUK1 GNAS CD24 CHP2 LAMB3 SRGN AHI1 NUSAP1 PDK4 RPL23A GSTP1 MT-CO1
83 ATP5MC1 TSPAN6 HSPH1 MT1H S100A16 VEGFA MCL1 UBE2S TYMP RPL13A RPA3 GNE
84 PSMA7 KCNQ1OT1 NASP LGALS4 SERPINB1 ERO1A NR4A1 HIST1H1E LINC02023 RPL30 CENPW AGR3
85 ATP6V1G1 GPRC5A LCN15 CFTR TXNIP TFF2 PAXBP1 PGP LRRC19 RPLP0 BEX3 AC005833.1
86 ATP5F1E RPL30 PTPRD TMEM59 IFI6 NEAT1 EPHB3 ANLN EDN3 TMSB10 PARK7 NXPE4
87 PSMB1 HSPB1 SLC29A1 SRI TM4SF1 GDF15 KCNQ1OT1 SIVA1 CCL28 LGALS3 MRPS34 MIA3
88 PYCARD ELF3 RAD21 DSG2 CLIC1 SLC6A8 AKAP9 SRSF7 APOBR HINT1 BIRC5 JUN
89 SSBP1 NUDT4 HMGB2 IFI16 PDP1 MUC13 HNRNPU YBX1 MYLK RPS15A RPL10 BTG2
90 GTF3A RNF213 MACC1 SNORC FTH1 ATF4 HJURP CLDN8 RPL29 TPI1 NEDD4L
91 PPDPF RPL10A ACTG1 LIMA1 NOXO1 ANKRD36C CENPH SEMA6A ACAT2 PEBP1 AGR2
92 QPRT NCOA7 RIF1 GALNT7 CD81 RPL13A TUBB4B C11orf86 ZFAS1 NDUFA4 GALNT7
93 SUB1 EFNB2 PCCA DUOX2 MRPL41 HIST1H2AC CCT6A TMEM236 HSD17B12 DKC1 MFSD4A
94 PDIA6 ZBTB10 PTK7 PAPSS2 NDFIP1 RAB11FIP1 SRSF3 CASP5 P4HA1 SNRPG SMIM14
95 SLC25A5 RPL37 SRSF2 B4GALNT3 IDS BRD2 CACYBP SECTM1 RBCK1 CBX5 MUC5B
96 PRDX4 TAPBP PTBP3 PDK4 RHOV MUC5B RAD51AP1 SCIN RPS3A COL9A3 RPS4Y1
97 SEC61B LRRC75A ASPM SLC39A5 TINAGL1 RPS27 TFDP1 RSAD2 RPS20 LSM5 HMGCS2
98 NDUFB5 LAMB3 PTMA CD24 CDKN2A KLF4 PPM1G LYPD8 GGH LSM4 MT-ATP6
99 RPL31 ITGA2 SAPCD2 SQOR KRT20 REG3A ALYREF CCDC152 PSMB1 SIVA1 ARFGEF3
100 RPLP0 RBM39 HSPD1 PTGER4 TMBIM1 HIST1H1E EXOSC8 B3GALT5 ATP6V1G1 MCM3 MT-ND4